Did we miss the most important implication of last week's rebellion by Tory MPs? Many focused on the re-emergence of European splits – the like of which we haven't seen since John Major was prime minister and Oasis and Blur were at war for the No 1 spot. In a recent piece, I focused on David Cameron's inept management of the party. He has sometimes acted as if he owned the government and party rather than as a prime minister who is but first among equals.

But beneath the issue of Europe and party management we are witnessing the emergence of something altogether more important, interesting and long-lasting. We are seeing the shift away from a Commons controlled by the whips and towards an era of supercharged backbenchers – backbenchers who are much more responsive to their local electorates and who see chairmanship of a select committee as an attractive alternative to becoming a minister.

Contrary to the cartoon image of MPs slavishly following their party leaders' orders, the trend towards independent-mindedness has been happening for some time. Professor Philip Cowley of Nottingham University has catalogued how MPs in all parties have become increasingly rebellious.

Defying the whip is like cheating on your spouse. It's never done lightly the first time, but gets easier and easier. So I'm told, anyhow. While the government whips would probably like every MP to think of rebellion in the same moral terms as adultery, the truth is that voters love the idea of independent MPs. They love the Ann Widdecombes and Tony Benns of politics who speak their mind.

Last week many Tory MPs crossed the Rubicon and they'll find it easier to rebel second, third and fourth times. Despite every kind of stick and carrot, 81 voted against the government on Europe. Another 40 threatened to do so on the issue of knife crime, but before they could do so the government U-turned. We've got to a place where the backbenches do not fear the government whips, but the government fears its backbenches. That's a very uncomfortable place for an administration that's only 18 months old.

There are many reasons why this phenomenon has suddenly taken off in Conservative ranks. Many Tory MPs feel at least as loyal to their party's manifesto as to the coalition agreement and they are forming groups to advance their concerns on crime, tax, Lords reform and other issues that motivate the Conservative base. Given the phalanx of Liberal Democrat ministers, Cameron has fewer frontbench positions with which to reward MPs. Tory MPs have noticed and concluded that they might as well focus on the concerns of their marginal constituencies. This is especially true for those facing difficult boundary reselections.

I was not optimistic about John Bercow's speakership but he has been an important part of this phenomenon. The legislature is rising from its knees under his watch. He gives more time to backbenchers' questions and grants more calls for ministers to make emergency statements. Backbenchers have power again.

In this brave new world, Downing Street's tolerance for dissent has to be higher. One rebellion can no longer be a red-card offence. If every MP who rebelled was cast into the darkness the government would be creating a permanent mutinous cell within its ranks. At the earliest opportunity it will need to rehabilitate a few of "the 81". It can only manage these changes, however. They are not reversible. The House of Commons is becoming more like the US House of Representatives.

By the end of this parliament there will probably be 70 or 80 MPs like Douglas Carswell, Zac Goldsmith and Sarah Wollaston, who don't see themselves as ministers-in-waiting but as servants of their constituencies. They are the most interesting feature of this new parliament and if the euro wasn't enough, they are another nightmare for Cameron.